EMPIAR-10171 - CryoET of apoferritin with 0.5 mM TCEP single particle with spot-to-plunge time of 170ms [multiple data sets in MRC and DYNAMO TBL AND OMD FILES formats]

EMPIAR-10171

CryoET of apoferritin with 0.5 mM TCEP single particle with spot-to-plunge time of 170ms [multiple data sets in MRC and DYNAMO TBL AND OMD FILES formats]

Publication:

Reducing effects of particle adsorption to the air-water interface in cryoEM

Noble AJ, Wei H, Dandey VP, Zhang Z, Potter CS, Carragher B

BioRxiv (---)

DOI: 10.1101/288340

Related EMDB entry:

EMD-7627

Deposited:

2018-04-03

Released:

2018-04-05

Last modified:

2018-04-05

Imageset size:

31.62 GB

Imageset DOI:

10.6019/EMPIAR-10171

Experimental metadata:

Download xml json

Contains:

tilt series
particle picking

Image Sets

1. Tilt-series image stacks

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 4984)

Pixel type:

SIGNED 16 BIT INTEGER

Pixel spacing:

(2.34, 2.34)

Details:

Not frame-aligned.
.mdoc files included.

Files:

Archives and downloads the selected files into an uncompressed zip file.

Depending on the number and size of files to be downloaded, this can take an enormous amount of time. Also, this feature is unstable and may not work properly, and checksums of downloaded files are not verified.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

2. Manual particle picking in Dynamo

Category:

particle picking

Image format:

DYNAMO TBL AND OMD FILES

No. of images or tilt series:

Image size:

(None, None)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(None, None)

Details:

Binned by 4 manual particle picking of the series0001 tomogram using Dynamo. Manual picking was performed to accurately distinguish between particles adsorbed to the air-water interfaces, non-adsorbed particles, and particles over or adsorbed to carbon.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

3. Appion-Protomo tilt-series alignments

Category:

tilt series

Image format:

MRC

No. of images or tilt series:

Image size:

(3712, 4984)

Pixel type:

32 BIT FLOAT

Pixel spacing:

(2.34, 2.34)

Details:

Includes a full tilt-series alignment run for each tilt-series. To view properly, navigate to the protomo_alignments folder in Appion-Protomo.

Files:

Archives and downloads the selected files into an uncompressed zip file.

We recommend using rsync, aspera, globus, etc.

Download a list of selected files.

It is possible to download files by specifying the file list with rsync command, etc.

rsync -av --files-from=(path-to-filelist) rsync://empiar.pdbj.org/empiar/archive (path-to-destination)

Browse All Files

Quick Links

Talks and Tutorials

EMPIAR Quick tour

Statistics

Publications

Re-use case study

EMPIAR in the news

Claim entries to your ORCiD

COVID-19 Data Portal

EMDB

PDBe

BioImage Archive

EMNavigator@PDBj

PDBj

RCSB@PDBj

EMDataResoruce@RCSB,EMDB,NCMI

Citations

Small LEA proteins mitigate air-water interface damage to fragile cryo-EM samples during plunge freezing.

Abe KM, Li G, He Q, Grant T, Lim CJ. (2024)

Outer membrane protein assembly mediated by BAM-SurA complexes.

Fenn KL, Horne JE, Crossley JA, Böhringer N, Horne RJ, Schäberle TF, Calabrese AN, Radford SE, Ranson NA. (2024)

Ubiquitinated histone H2B as gatekeeper of the nucleosome acidic patch.

Hicks CW, Rahman S, Gloor SL, Fields JK, Husby NL, Vaidya A, Maier KE, Morgan M, Keogh MC, Wolberger C. (2024)

Molecular recognition of an odorant by the murine trace amine-associated receptor TAAR7f.

Gusach A, Lee Y, Khoshgrudi AN, Mukhaleva E, Ma N, Koers EJ, Chen Q, Edwards PC, Huang F, Kim J, Mancia F, Veprintsev DB, Vaidehi N, Weyand SN, Tate CG. (2024)

The novel ribosome biogenesis inhibitor usnic acid blocks nucleolar pre-60S maturation.

Kofler L, Grundmann L, Gerhalter M, Prattes M, Merl-Pham J, Zisser G, Grishkovskaya I, Hodirnau VV, Vareka M, Breinbauer R, Hauck SM, Haselbach D, Bergler H. (2024)

See all citations

Protein Data Bank Japan News

[2024-11-06]

404 new PDB entries have been released on 2024-11-06.

[2024-11-01]

A new portal integrating genome variants and protein structures has released

[2024-10-30]

[wwPDB] Deprecation of FTP File Download Protocol on November 1, 2024

[2024-10-25]

PDBj luncheon seminar at APBJC 2024

[2024-10-17]

[wwPDB] The Nobel Prize in Chemistry 2024